I don’t know if this helps. I repeated the process two more times and get the following error.
Thanks in advance, George
> PROTEIN=loadpdb 3n7h.pdb
Loading PDB file: ./3n7h.pdb
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 156
!FATAL: Message: VarArrayDestroy: VARARRAY is NULL!
!ABORTING.
On 1Dec, 2014, at 5:06 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Dan,
>
> I’m running AmberTools 13. I’ve prepared numerous parameter files in the last few days without problem.
>
> In fact, I’ve run a 100ns MD simulation and what I’m trying to do is to generate new parameter files keeping a conserved water molecule in the topology of the receptor. The reason for this is to run MMPBSA making sure that the water molecule is not stripped.
>
> Regards
>
> George
>
> On 1Dec, 2014, at 5:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> What version of AmberTools are you running, and what updates have been
>> applied? Do all tests pass?
>>
>> -Dan
>>
>> On Monday, December 1, 2014, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> I’m trying to generate parameter files for a protein.
>>>
>>> lteap generates top and crd files for the COMPLEX. The complex has two
>>> ligands and one water molecule
>>>
>>> saveamberparm COMPLEX 3n7h_de4.top 3n7h_de4.crd
>>> Checking Unit.
>>> WARNING: The unperturbed charge of the unit: -9.002004 is not zero.
>>>
>>> -- ignoring the warning.
>>>
>>> Building topology.
>>> Building atom parameters.
>>> Building bond parameters.
>>> Building angle parameters.
>>> Building proper torsion parameters.
>>> Building improper torsion parameters.
>>> total 406 improper torsions applied
>>> Building H-Bond parameters.
>>> Incorporating Non-Bonded adjustments.
>>> Not Marking per-residue atom chain types.
>>> Marking per-residue atom chain types.
>>> (Residues lacking connect0/connect1 -
>>> these don't have chain types marked:
>>>
>>> res total affected
>>>
>>> CVAL 1
>>> DE3 1
>>> DE4 1
>>> NASP 1
>>> WAT 1
>>> )
>>> (no restraints)
>>>
>>>
>>> The receptor has one ligand and one water molecule. But when I try to load
>>> the protein and generate parameters I get. Any suggestions how to overcome
>>> this problem would be most welcome
>>>
>>> /Programs/amber12/bin/tleap: line 17: 1888 Segmentation fault: 11
>>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
>>> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <javascript:;>
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Dec 01 2014 - 12:30:04 PST
